As for what a multi crew licence holder does when their computer controlled aircraft stops behaving as it should, like the BA 777 whose thrust levers didn't respond at LHR, I'll leave that to your imagination. My guess is they will look over their shoulder to see if they are in the sim.
The MPL cadets did spend considerable time in 'real' aircraft, including first solo, navigation and instrument flying.
Don't ask me for specifics, I wasn't involved, however you may all want to do your research to see what Stanley and his mates went through. Scoring 100% on ATPL subjects wasn't too bad either.